rs932425

Variant names:

• chr20-39244967-A-G
• rs932425
• ENST00000772859.1:n.458+25219A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000772859.1(ENSG00000300599):​n.458+25219A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,102 control chromosomes in the GnomAD database, including 5,199 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5199 hom., cov: 32)
• Consequence: ENSG00000300599 ENST00000772859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 0 publications found

Genes affected

ENSG00000300599 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300599	ENST00000772859.1	n.458+25219A>G		intron_variant	Intron 2 of 2
ENSG00000300599	ENST00000772860.1	n.313+25219A>G		intron_variant	Intron 3 of 3
ENSG00000300599	ENST00000772861.1	n.313+25219A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39005 AN: 151984 Hom.: 5187 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.257 AC: 39047 AN: 152102 Hom.: 5199 Cov.: 32 AF XY: 0.260 AC XY: 19347 AN XY: 74354

African (AFR) AF: 0.213 AC: 8837 AN: 41512

American (AMR) AF: 0.290 AC: 4433 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1923 AN: 5158

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4814

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17524 AN: 67978

Other (OTH) AF: 0.243 AC: 512 AN: 2106

Alfa AF: 0.238 Hom.: 1029

Bravo AF: 0.253

Asia WGS AF: 0.398 AC: 1382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.64
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs932425; hg19: chr20-37873610;